The Ferryman

ToxBank Infrastructure - paper available in Open Access

The following publication is now available in Open Access:

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

Pekka Kohonen, Emilio Benfenati, David Bower, Rebecca Ceder, Michael Crump, Kevin Cross, Roland C. Grafström, Lyn Healy, Christoph Helma, Nina Jeliazkova, Vedrin Jeliazkov, Silvia Maggioni, Scott Miller, Glenn Myatt, Michael Rautenberg, Glyn Stacey, Egon Willighagen, Jeff Wiseman, and Barry Hardy

Molecular Informatics
Special Issue: Advances in Computational Toxicology

Volume 32, Issue 1, pages 47–63, January 2013

http://onlinelibrary.wiley.com/doi/10.1002/minf.201200114/abstract

Removal of master control gene function in stem cells

Removal of master control gene function in stem cells allows expression of normally suppressed genes, hence expanding potential clinical use of the cells.

The control gene - microRNA 126 (miR-126) -- normally governs the expression of hundreds of other genes by keeping them silenced, which in turn keeps the stem cells in a non-dividing dormant state. Design and introduction of a viral vector was able to shut down the control gene, after which was observed a long-term expansion of the blood stem cells without exhaustion or malignant transformation.

http://www.sciencedaily.com/releases/2012/11/121108141024.htm

Free downloads are available on new safety evaluation research aiming to replace animal testing

Free book downloads are available on our predictive toxicology research
carried out within the public private partnership of SEURAT (Safety
Evalua tion Ultimately Replacing Animal Testing) -1 (where 1 indicates the first phase of 5 years).
 
The SEURAT-1 annual books called "Towards the replacement of in vivo
repeated dose systemic toxicity testing", aim to inform policy makers
about scientific progress relevant to the implementation of European
Directives and Regulations and about essential gaps in knowledge
corresponding to research needs.

http://www.seurat-1.eu/pages/library/seurat-1-annual-report.php

Tamoxifen pathway crosstalk point

Tamoxifen cancer resistance may be driven by a novel molecular "crosstalk" point between the estrogen and HER2 signaling pathways

http://www.firstwordpharma.com/node/1030352

A Shared Moment of Great Happiness

Barry Hardy and Spela Predan, Just Married.

 

OpenTox 2011 Technical Reports

The following #OpenTox 2011 technical reports in predictive toxicology are available for downloading:

OpenTox D1.4 Report on Evaluation of the Final Implementation

OpenTox D2.4 Report on Final Framework

OpenTox D3.4 Report on Final Database with Additional Content

OpenTox D4.3 Report on Final Version of (Q)SAR algorithms

OpenTox D5.3 Report on Validation Against Confidential Data

OpenTox D5.4 Report on Final Validation Routines with Facilities to Validate Against Confidential Data

ToxBank wiki open

I am happy to inform that we have now made the first version of the ToxBank wiki (wiki.toxbank.net) open.

The first version of this wiki contains information on reference compounds which will be used to probe mechanisms of toxicity as carried out by experiments and modelling under the SEURAT-1 predictive toxicolgy research program. The long term strategic target of this program is "Safety Evaluation Ultimately Replacing Animal Testing". We make this resource public to provide useful information in support of other research projects with similar goals and to foster cross-fertilisation, alignment and collaboration.

I will be happy to receive your feedback and suggestions on this new resource.

Barry Hardy

barry.hardy -!(at)- douglasconnect.com

https://www.facebook.com/barry.hardy3

Predictive Toxicology Ontology Perspectives and Roadmap

Re: #OpenTox, ontology, new predictive toxicology systems

The following papers are now available from the new issue of Altex:

Toxicology ontology perspectives
This article provides an overview of some of the leading developments in
incorporating ontology into new knowledge-based systems in predictive toxicology.

http://www.altex.ch/en/index.html?id=16&aid=3

A toxicology ontology roadmap
In this article we lay out the main justifications and needs for ontology
development to enable the building of interoperable predictive toxicology systems
and services for industry to design and test safer products.

http://www.altex.ch/en/index.html?id=16&aid=2

OpenTox Toxicology Ontology Development

This article is just out online describing initial #OpenTox ontology work:

#OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337268/

#OpenTox - #Bioclipse Cloud article

The final version of our first #OpenTox - #Bioclipse paper on getting our tox cloud working with the Bioclipse workbench for interactive design for safety purposes is now available in open access. See http://www.biomedcentral.com/1756-0500/4/487